Understanding VCF format

VCF is the standard file format for storing variation data. It is used by large scale variant mapping projects such as IGSR. It is also the standard output of variant calling software such as GATK and the standard input for variant analysis tools such as the VEP or for variation archives like EVA.

VCF is a preferred format because it is unambiguous, scalable and flexible, allowing extra information to be added to the info field. Many millions of variants can be stored in a single VCF file. 

VCF files are tab delimited text files. Here is an example of a variant in VCF (Figure 12) as viewed in a spreadsheet:

The spreadsheet has a column for each of the following:
#CHROM
POS
ID
REF
ALT 
QUAL
FILTER
INFO
FORMAT
Figure 12 An example of a VCF file.

VCF file structure

To learn more, take a look at the VCF specifications.